Diet is known to modify the composition of the gut microbiota. However, few studies have been conducted to assess the relationship between diet and the gut microbiota in infants during the complementary feeding period, or in young children. Associated with the rapid advancement of technology in the gut microbiota field, several bioinformatic data handling processes have been developed to be used to identify links between diet and the gut microbiota. While many common statistical methods have been used, the most appropriate method to determine associations between dietary components and microbiota composition is open to debate.

The overall aim of this thesis was to examine the effects of diet on the composition of the gut microbiota in children using appropriate nutritional, microbiological, and statistical methods, by answering three key questions:

1. How is diet during the complementary feeding period associated with children’s subsequent gut microbiota composition at 12 months?

2. Can a food frequency questionnaire (FFQ) measure intake of dietary components thought to influence the composition of the gut microbiota?

3. In what ways is diet associated with the composition of the gut microbiota at 5 years of age?

Chapters 3 and 4 examine the effect of feeding method at 7 months of age on the composition of the gut microbiota at 12 months. The composition of the gut microbiota in 74 participants participating in a randomised controlled trial (the ‘Baby-Led Introduction to SolidS (BLISS) study’) was determined by sequencing 16S rRNA genes, and 3-day weighed diet records (WDR) were used to estimate dietary intake. In a novel approach to analysing gut microbiota data, mediation models were used to demonstrate that 29% and 25% of the link between feeding method (BLISS vs Control) and alpha diversity at 12 months could be explained by lower ‘fruit, vegetables, nuts and legumes’ and dietary fibre intake in the BLISS group at 7 months.

Chapter 5 focuses on determining the relative validity and reproducibility of an FFQ for assessing amount and ranking of intakes of nutrients and foods that have been reported to influence the composition of the gut microbiota. One hundred parent-child pairs completed a 3-day WDR and an FFQ on two separate occasions four weeks apart. The FFQ was found to have acceptable validity for ranking intakes of energy, carbohydrate, dietary fibre, total non-starch polysaccharides (NSP), and insoluble NSP, when compared with the 3-day WDR, and very good reproducibility when measured over four weeks. The FFQ was also suitable for assessing mean absolute intake of carbohydrate, dietary fibre, and total NSP.

Chapters 6 and 7 examine the relationship between diet (measured using the validated FFQ) and gut microbiota composition (determined by sequencing 16S rRNA genes) at 5 years of age. Data from 319 participants from the ‘Prevention of Overweight in Infancy (POI) study’ were available at 5 years of age. Using compositional principal component analysis (PCA), 3 gut microbiota profiles were identified. Profile 2 (positive loadings on Bacteroides; negative loadings on uncultured Christensenellaceae and Ruminococcaceae) and profile 3 (positive loadings on Faecalibacterium, Eubacterium and Roseburia) were independently associated with body mass index (BMI) z-score, and dietary components (fibre, total NSP, and ‘meat, fish, poultry’ intake), respectively.

These results show that in older infants and young children, certain dietary components (‘fruit and vegetables’, fibre, total NSP and ‘meat, fish, poultry’) and BMI z-scores were associated with aspects of the gut microbiota (alpha diversity and gut microbiota profile scores). Collectively, the studies in this thesis demonstrate the utility of a validated FFQ as a dietary assessment tool for use in large studies assessing diet and the gut microbiota, and the usefulness of two different statistical methods (mediation, and compositional PCA) to determine linkages between food components and the gut microbiota. These robust methods further our understanding of the relationships between diet and the gut microbiota in infants and young children.